rs9528094

Positions:

• chr13-60274914-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000448913.1(TARDBPP2):​n.139C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.531 in 1,411,864 control chromosomes in the GnomAD database, including 201,653 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.49 (18729 hom., cov: 32)
  • Exomes 𝑓: 0.54 (182924 hom.)
• Consequence: TARDBPP2 ENST00000448913.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.15

Genes affected

TARDBPP2 (HGNC:39848): (TARDBP pseudogene 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TARDBPP2	ENST00000448913.1	n.139C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74586 AN: 151826 Hom.: 18711 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.444

GnomAD4 exome AF: 0.536 AC: 675731 AN: 1259920 Hom.: 182924 Cov.: 22 AF XY: 0.536 AC XY: 339846 AN XY: 634050

Gnomad4 AFR exome AF: 0.378

Gnomad4 AMR exome AF: 0.475

Gnomad4 ASJ exome AF: 0.395

Gnomad4 EAS exome AF: 0.582

Gnomad4 SAS exome AF: 0.550

Gnomad4 FIN exome AF: 0.550

Gnomad4 NFE exome AF: 0.547

Gnomad4 OTH exome AF: 0.504

GnomAD4 genome AF: 0.491 AC: 74654 AN: 151944 Hom.: 18729 Cov.: 32 AF XY: 0.493 AC XY: 36619 AN XY: 74254

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.459

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.547

Gnomad4 OTH AF: 0.444

Alfa AF: 0.522 Hom.: 37849

Bravo AF: 0.478

Asia WGS AF: 0.464 AC: 1616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	8.3
DANN	Benign	0.73

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9528094; hg19: chr13-60849048;